From 4c32e93b898b8089a7ce27f5a04a4c8f1600c780 Mon Sep 17 00:00:00 2001
From: max <you@example.com>
Date: Sun, 27 Oct 2019 18:52:52 +0100
Subject: [PATCH] minimap2 build

---
 __pycache__/checkHitlist.cpython-36.pyc | Bin 0 -> 4247 bytes
 __pycache__/globalVars.cpython-36.pyc   | Bin 0 -> 4830 bytes
 __pycache__/gpma.cpython-36.pyc         | Bin 0 -> 5537 bytes
 __pycache__/merging.cpython-36.pyc      | Bin 0 -> 6082 bytes
 __pycache__/splitReads.cpython-36.pyc   | Bin 0 -> 2533 bytes
 globalVars.py                           |   3 +--
 main.py                                 |  34 +++---------------------
 7 files changed, 4 insertions(+), 33 deletions(-)
 create mode 100644 __pycache__/checkHitlist.cpython-36.pyc
 create mode 100644 __pycache__/globalVars.cpython-36.pyc
 create mode 100644 __pycache__/gpma.cpython-36.pyc
 create mode 100644 __pycache__/merging.cpython-36.pyc
 create mode 100644 __pycache__/splitReads.cpython-36.pyc

diff --git a/__pycache__/checkHitlist.cpython-36.pyc b/__pycache__/checkHitlist.cpython-36.pyc
new file mode 100644
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diff --git a/globalVars.py b/globalVars.py
index 32c75ca..dda5a3d 100644
--- a/globalVars.py
+++ b/globalVars.py
@@ -199,12 +199,11 @@ class mySCAF:
 
 
 # function to initialize global variables
-def init(out, sL, mL, mO, mI, t, mSV, bPATH, mPATH):
+def init(out, sL, mL, mO, mI, t, mSV):
     global largestContig, distError, outDir, splitLen, minOverlap, minLinks
     global minIdent, threads, contsMerged, contLenDICT, contDICT, mergedDICT, readHash
     global contigGR, adjustDICT, gapDICT, eDICT, edgeDICT
     global blastCounter, poserrorHASH, minSVL
-    global blastP, minimap2P 
 
     global insE, delE, invE, mjE, goodE
     insE={}
diff --git a/main.py b/main.py
index 83ed55f..a3cb7b7 100755
--- a/main.py
+++ b/main.py
@@ -74,31 +74,7 @@ class mySCAF:
 ###functions#######################
 ###################################
 
-# function to parse the config file containing the paths to
-# blastn and minimap2
-def parsePATHs():
-    scriptPath=sys.argv[0].rstrip("main.py")
-    configReader=open("%s/config.txt"%scriptPath)
-    minimap2Path=""
-    blastnPath=""
-    for line in configReader:
-        if not line.startswith("#"):
-            if line.startswith("MINIMAP2"):
-                minimap2Path = line.strip().split("=")[-1]
-            elif line.startswith("BLASTN="):
-                blastnPath = line.strip().split("=")[-1]
-    if minimap2Path=="":
-        print("Error no entry for minimap2 path in config.txt found - exiting...")
-        exit()
-    if blastnPath=="":
-        print("Error no entry for blastn path in config.txt found - exiting...")
-        exit()
-    configReader.close()
-    #print("minimap path: %s"%(minimap2Path))
-    #print("blastn path: %s"%(blastnPath))
-    
-    return minimap2Path, blastnPath
-    
+ 
 #function to reverse complement a sequence
 def reverseComplement(seq):
     old = "ACGT"
@@ -110,9 +86,7 @@ def runMinimap2(nThreads, mapMode, inFA, inFQ, outPAF):
     scriptPath=sys.argv[0].rstrip("main.py")
     try:
         subprocess.call("%s/minimap2/minimap2 -t %i -x %s %s %s> %s" %
-                        (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True, stdout=DEVNULL, stderr=subprocess.STDOUT)
-        #subprocess.call("%s/minimap2/minimap2 -t %i -x %s %s %s> %s" %
-        #                (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True)
+                        (scriptPath, nThreads, mapMode, inFA, inFQ, outPAF), shell=True, stdout=DEVNULL)
     except:
         print("Problem running minimap2 - check if its properly set up")
 
@@ -800,13 +774,11 @@ def removeTMPfiles():
 def run(genome, nobreak, curIter):
     # create output directory if it not exists already
     subprocess.call("mkdir -p %s" % (args.outdir), shell=True)
-    
-    miniPATH, blPATH = parsePATHs()
 
     # initlaiye global variables
     if curIter > 0:
         tempStore=globalVars.readHash
-    globalVars.init(args.outdir, args.size, args.minlinks, args.minoverlap, args.minident, args.threads, args.minSVLen, blPATH, miniPATH)
+    globalVars.init(args.outdir, args.size, args.minlinks, args.minoverlap, args.minident, args.threads, args.minSVLen)
     
     if curIter>0:
         globalVars.readHash=tempStore
-- 
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